Jax in the back of a police van? I somehow thought this was the finale to the whole series, but I might be wrong.
I actually don't remember anything from when I watched this series. I could rewatch it, but I don't know.
I just finished binge-watching it.
Jax wound up in prison/jail twice, only briefly both times. I think the particular scene you're referring to was the first time when a bunch of the MC ended up in prison. I think the scene was of them being transported to prison all dressed up in their orange jumpsuits. IIRC it was deliberate on their part... some sort of plan they had in play, but they had to be in prison to execute it. Clay was still leading the MC at this point.
The second time (end of S4? S5?), Jax makes a deal to take the blame for some crime or other that involved the whole club. There's an emotional scene where everyone is weeping as they all say good-bye to each other. Of course, in the very first ep of the next season he's out again due to a lack of evidence, some technicality or similar.
No specific spoilers if you want to watch it again, but the finale to the series is dramatic... and final.